Specific and broad-spectrum antibacterial effectors of type VI secretion system drive competition of Stenotrophomonas rhizophila against bacteria from seed microbiota

The type VI secretion system (T6SS) is a bacterial weapon that injects deadly effectors (T6Es) directly into a target competitor encountered in a microbial community. Stenotrophomonas rhizophila CFBP13503 ( Sr ), a seed-borne bacterium, uses its T6SS to target a wide range of other bacterial species, impacting seed microbiota assembly, and controlling phytopathogen transmission from seed to seedling. How the large T6E repertoire and other features contribute to S. rhizophila ’s impact was investigated. Using transcriptional and translational reporters combined with fluorescence microscopy and proteomic approaches, we confirmed the expression and production of nine effectors secreted by a highly dynamic T6SS. This resulted in killing target cells through four major cell death phenotypes, with different frequencies depending on the target species. The systematic deletion of single effectors revealed a general synergy in killing a wide range and diverse seed-borne bacteria, but also a target-specific killing. Comparative genomics suggests that Sr -T6Es are commonly shared in the Stenotrophomonas genus diversity but are also highly plastic and acquired from diverse bacterial families. Inversely, T6SS-resistance markers, such as capsule and orthologous immunities, are weakly distributed in seed microbiota, and do not explain resistance to Sr -T6SS. Importantly, two amidases explained the major T6SS antibacterial activity, and only the Rhs-fused effector targeted a Gram-positive bacterium. Our work depicts the generalist or specific role of each effector in the S. rhizophila T6SS activity targeting either aggressive, closely related, broad, or Gram-positive bacteria from seed microbiota. IMPORTANCE The type VI secretion system (T6SS) is largely distributed among seed-borne bacteria. However, it remains important to understand how this interbacterial competition weapon could provide a competitive advantage for some strains and influence microbiome assembly during seed-to-seedling transmission. The Stenotrophomonas rhizophila CFBP 13503 strain, a seed-associated bacterium, cumulated several T6SS features like a constitutive and highly dynamic T6SS associated with 12 putative antibacterial T6Es that shape microbiota assembly through broad and strain-specific targeting within seed microbiota. Hence, genomic analysis suggests that S. rhizophila T6E repertoire is adaptive thanks to genetic gain and loss or through gene regulation. In the context of microbiome engineering, the relevance of this study is to highlight the need to associate broad-effective and competitive S. rhizophila strains, as well as T6SS-resistant strains, in bacterial synthetic communities as seed inoculum against phytopathogens.